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author nick
date Thu, 02 Feb 2017 19:50:18 -0500
parents 675a8370675b
children 8ef925264516
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1 <?xml version="1.0"?>
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2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.5">
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3 <description>from duplex sequencing alignments</description>
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4 <requirements>
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5 <requirement type="package" version="0.5">duplex</requirement>
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6 <requirement type="set_environment">DUPLEX_DIR</requirement>
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7 <!-- TODO: require Python 2.7 -->
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python "\$DUPLEX_DIR/dunovo.py" -r $min_reads -q $qual_thres -F $qual_format '$input'
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11 #if $keep_sscs:
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12 --sscs-file sscs.fa
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13 #end if
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14 > duplex.fa
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15 && python "\$DUPLEX_DIR/utils/outconv.py" duplex.fa -1 '$dcs1' -2 '$dcs2'
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16 #if $keep_sscs:
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17 && python "\$DUPLEX_DIR/utils/outconv.py" sscs.fa -1 '$sscs1' -2 '$sscs2'
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18 #end if
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="input" type="data" format="tabular" label="Aligned input reads" />
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23 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
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24 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
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25 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
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26 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
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27 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
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28 </param>
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29 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
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30 </inputs>
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31 <outputs>
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32 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
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33 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
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34 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">
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35 <filter>keep_sscs</filter>
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36 </data>
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37 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)">
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38 <filter>keep_sscs</filter>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input" value="families.msa.tsv"/>
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44 <output name="dcs1" file="families.cons_1.fa"/>
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45 <output name="dcs2" file="families.cons_2.fa"/>
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46 </test>
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47 </tests>
21
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48 <citations>
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49 <citation type="bibtex">@article{Stoler2016,
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50 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
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51 doi = {10.1186/s13059-016-1039-4},
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52 issn = {1474-760X},
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53 journal = {Genome biology},
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54 number = {1},
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55 pages = {180},
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56 pmid = {27566673},
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57 publisher = {Genome Biology},
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58 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
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59 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
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60 volume = {17},
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61 year = {2016}
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62 }</citation>
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63 </citations>
19
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64 <help>
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65
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66 **What it does**
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67
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68 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
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69
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70 -----
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71
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72 **Input**
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73
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74 This expects the output format of the "Align families" tool.
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75
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76 -----
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77
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78 **Output**
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79
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80 This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
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81
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82 </help>
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83 </tool>